aPPRove – Accurate Prediction of RNA and Pentatricopeptide Repeat Protein Binding

aPPRove

:: DESCRIPTION

aPPRove is a computational tool that predicts the interaction of a PPR with its RNA binding site.

::DEVELOPER

SEQ Development Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

aPPRove

:: MORE INFORMATION

Citation

New Phytol. 2011 Jul;191(1):37-47. doi: 10.1111/j.1469-8137.2011.03746.x. Epub 2011 May 9.
The evolution of RNA editing and pentatricopeptide repeat genes.
Fujii S1, Small I.

PANTHER – Novel tool to Predict Small Molecule Binding into Proteins

PANTHER

:: DESCRIPTION

PANTHER is a rapid virtual screening method that can evaluate tens of millions of small molecules into selected protein target in 24 hours

::DEVELOPER

Computational Bioscience Laboratory, University of Jyväskylä

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Python

:: DOWNLOAD

 PANTHER

:: MORE INFORMATION

Citation

Ultrafast protein structure-based virtual screening with Panther.
Niinivehmas SP, Salokas K, Lätti S, Raunio H, Pentikäinen OT.
J Comput Aided Mol Des. 2015 Sep 25.

JASPAR 2020 – Transcription Factor Binding Profile Database

JASPAR 2020

:: DESCRIPTION

JASPAR is the largest open-access database of matrix-based nucleotide profiles describing the binding preference of transcription factors from multiple species.

::DEVELOPER

The Wasserman Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/MacOsX/Linux
  • R package/BioConductor/BioPython

:: DOWNLOAD

  JASPAR for BioConductor

:: MORE INFORMATION

Citation

Fornes O, Castro-Mondragon JA, Khan A, et al.
JASPAR 2020: update of the open-access database of transcription factor binding profiles.
Nucleic Acids Res. 2019; doi: 10.1093/nar/gkz1001

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles.
Mathelier A, Zhao X, Zhang AW, Parcy F, Worsley-Hunt R, Arenillas DJ, Buchman S, Chen CY, Chou A, Ienasescu H, Lim J, Shyr C, Tan G, Zhou M, Lenhard B, Sandelin A, Wasserman WW.
Nucleic Acids Res. 2013 Nov 4.

BeAtMuSiC 1.0 – Prediction of Binding Affinity Changes upon Mutations

BeAtMuSiC 1.0

:: DESCRIPTION

The BeAtMuSiC program evaluates the change in binding affinity between proteins (or protein chains) caused by single-site mutations in their sequence.

::DEVELOPER

Service de Biomodélisation, Bioinformatique et Bioprocédés (3BIO)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W333-9. doi: 10.1093/nar/gkt450. Epub 2013 May 30.
BeAtMuSiC: Prediction of changes in protein-protein binding affinity on mutations.
Dehouck Y, Kwasigroch JM, Rooman M, Gilis D.

GraphProt 1.1.4 – Modeling Binding preferences of RNA-binding Proteins

GraphProt 1.1.4

:: DESCRIPTION

GraphProt can be used for modeling binding preferences of RNA-binding proteins from high-throughput experiments such as CLIP-seq and RNAcompete.

::DEVELOPER

Chair for Bioinformatics Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 GraphProt

:: MORE INFORMATION

Citation

Genome Biol. 2014 Jan 22;15(1):R17. [Epub ahead of print]
GraphProt: modeling binding preferences of RNA-binding proteins.
Maticzka D, Lange SJ, Costa F, Backofen R.

MultiTF-PPI – Competitive Transcription Factor Binding Prediction

MultiTF-PPI

:: DESCRIPTION

MultiTF-PPI is a probabilistic protein-protein interaction guided method for competitive transcription factor binding prediction.

::DEVELOPER

Computational systems biology group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Matlab

:: DOWNLOAD

MultiTF-PPI

:: MORE INFORMATION

NetMHCII 2.3 – Predict Binding of Peptides to MHC class II Alleles

NetMHCII 2.3

:: DESCRIPTION

NetMHCII predicts binding of peptides to HLA-DR, HLA-DQ, HLA-DP and mouse MHC class II alleles using articial neuron networks.
Predictions can be obtained for 14 HLA-DR alleles covering the 9 HLA-DR supertypes, six HLA-DQ, six HLA-DP, and two mouse H2 class II alleles.
The prediction values are given in nM IC50 values, and as a %-Rank to a set of 1,000,000 random natural peptides. Strong and weak binding peptides are indicated in the output.

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

NetMHCII

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2009 Sep 18;10:296.
NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction.
Nielsen M, Lund O.

BaalChIP 1.12.0 – Bayesian Analysis of Allele-specific Transcription Factor Binding in Cancer Genomes

BaalChIP 1.12.0

:: DESCRIPTION

BaalChIP ( Bayesian Analysis of Allelic imbalances from ChIP-seq data) corrects for the effect of background allele frequency on the observed ChIP-seq read counts jointly analyses multiple ChIP-seq samples across a single variant.

::DEVELOPER

the Markowetz lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R
  • BioCOnductor

:: DOWNLOAD

BaalChIP

:: MORE INFORMATION

Citation

Genome Biol, 18 (1), 39 2017 Feb 24
BaalChIP: A probabilistic framework for reconstructing intra-tumor phylogenies
I. de Santiago, W. Liu, K. Yuan, M. O’Reilly, CS. Chilamakuri, B. Ponder, K. Meyer, F. Markowetz

CCmiR – Prediction of miRNA Competitive / Cooperative Binding

CCmiR

:: DESCRIPTION

CCmiR is a software for competitive and cooperative microRNA binding prediction

::DEVELOPER

Hu Lab – Data Integration and Knowledge Discovery @ UCF

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

CCmiR

:: MORE INFORMATION

Citation:

Bioinformatics. 2018 Jan 15;34(2):198-206. doi: 10.1093/bioinformatics/btx606.
CCmiR: a computational approach for competitive and cooperative microRNA binding prediction.
Ding J, Li X, Hu H.

mCross – Modeling RBP Binding Specificity by registering protein-RNA Crosslink Sites

mCross

:: DESCRIPTION

mCrossBase is a database of RNA-binding protein (RBP) binding motifs and crosslink sites defined jointly from CLIP data using a novel algorithm mCross

::DEVELOPER

Zhang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Feng et al. (2019),
Modeling the in vivo specificity of RNA-binding proteins by precisely registering protein-RNA crosslink sites.
Mol Cell. 74:1189-1204.E6.